The email message (envelope icon) in the upper left corner shows a number indicating notifications are available and even though the messages were cleared, the indicator still shows 1 (and in another case 2).
I have had a look and the notifications seem to be functioning. Because your site is live i didn't want to start creating messages so i can test it. Are you able to set up some notifications so i can see it happening.
I would also recommend clearing your browser cache to make sure it isn't the browser holding the cache from a previous session
